January 25, 2008

Current and Future

Database (CH)

Indexing vgd_common (JM; 1Q) Fully implement Taxonomy tables

(JO, DD; 2Q) Allow subspecies-level taxonomy Fix Dengue Fix HCV

Fully update Pluto.vgd_common with all patches (CH)

Data (CH)

Data releases Data Release 6.4 (JM; 1Q) Data Release 6.5 (SC; 2Q)

Continuous data release (JM; 4Q) Replication between Pluto and Gendb

Databases Automated annotation Correct handling of “missing”

information by web site

Reference Genomes (CH)

Define Curated strain RefSeq strain

Links from all VOCs orthologs Links to RefSeq and VBRC reference

BLAST (JM)

VBRC BLAST Processes (JM) Reevaluate process of storing all BLAST

data (2Q) Separate BLAST data into new db (2Q)

Add views to vgd_common Reassess BLAST XML Parsing tools

HCV BLAST (JO) Update HCV BLAST db (1Q) Move HCV BLAST from mars to VBRC

(2Q)

Protein information (JM, SC) Generate all figures on-the-fly

Genome maps (1Q) Hydrophobicity plots (3Q)

Get rid of dependence on GCG (3Q) Display aa location of any motif hit (2Q) Epitopes (SC)

Evaluate HCV epitopes: Why so many (JO) Epitope identification by taxonomy (2Q)

EC numbers (SC; 2Q) Polymerase Protease

HCV annotation (JO)

HCV genotyping Alignments

Generate View

Trees Generate View

Manual method for genotyping (2Q) Automated genotyping (4Q)

KDB (DD)

In production (1Q) Tie in with vgd_common (2Q)

Table/field relationships Annotation statistics updates

UVic annotation pipeline (CH; 2Q) VOCs

Better annotation InterPro

Identify location DO NOT delete genome/gene IDs

Curation (EK; continuous) Gene names

Consistent Meaningful Coordinate names in KDB with

vgd_common (CH, DD)

Controlled vocabularies (JO; 2008-2009) GO SO

Genome search and display(JO; 2008-2009) New search interface

Combine genome and gene Visualization

Genome maps Search results Variation Features

Epitopes Functional motifs

Web site (JM)

Genome maps (1Q) Create all on-the-fly

Add contract # to web site (1Q) Update documents (1Q)

July 2007 Progress Report Bug fixes (2Q) How well do filters handle taxonomy

updates/changes? (CH, DD; 2Q)

Help (JM, CG)

Online (1Q) Tutorials (3Q)

IOWG (EJL, CH)

Annotation Lists (1Q) GFF3 File formats (2Q)

Properly annotate mature peptides Properly annotate RNA processing

HCV (EJL)

Add LANL HCV advisory members to SWG (1Q)

Genome information (2Q) Contact SLU for data

ICTVdb (EJL)

Create link-outs (3Q)

NCBI Interactions (CH)

Links GenBank record parsing

Next Group Meeting

February 8th, 2008 2:30 – 4:30 AIDS Center Conference Room, BBRB

Room 256A Topic

KDB Presenter

Don Dempsey